|Publication number||US7858387 B2|
|Application number||US 10/426,226|
|Publication date||Dec 28, 2010|
|Filing date||Apr 30, 2003|
|Priority date||Apr 30, 2003|
|Also published as||CA2524249A1, CA2524249C, EP1618591A2, US20040219531, US20110056311, WO2004100207A2, WO2004100207A3|
|Publication number||10426226, 426226, US 7858387 B2, US 7858387B2, US-B2-7858387, US7858387 B2, US7858387B2|
|Inventors||Joseph L. DiCesare|
|Original Assignee||Perkinelmer Health Sciences, Inc.|
|Export Citation||BiBTeX, EndNote, RefMan|
|Patent Citations (33), Non-Patent Citations (13), Referenced by (1), Classifications (32), Legal Events (5)|
|External Links: USPTO, USPTO Assignment, Espacenet|
The invention relates to a method of analyzing a sample plate in mass spectrometry using a sample plate having a rough hydrophobic surface.
Matrix-assisted laser desorption and ionization mass spectrometry (MALDI-MS) is an important analytical tool for the study and identification of biomolecules, particularly proteins, peptides, and nucleic acids such as DNA and RNA.
MALDI-MS results in a mass spectrum that graphically identifies biomolecules according to peaks that correspond to the biomolecules' concentration and mass. Using a library of known peaks, the biomolecules can be identified.
Various methods exist for the preparation of samples for analysis by MALDI-MS, including the dried droplet method. In the dried droplet method an aqueous sample containing the subject biomolecule is mixed with an organic compound, the matrix, which is usually suspended in an easily evaporative aqueous-organic solvent. The resulting liquid mixture containing the biomolecule, the matrix, aqueous solution, and solvents is referred to herein as the specimen.
The specimen is applied to the sample plate in a predetermined target area and allowed to dry. As the solvent begins to evaporate, and the biomolecule and matrix become more concentrated, the matrix molecules crystallize from solution while drying on the sample plate. The resulting crystals entrap the biomolecules on and/or within the crystals and in due course deposit on the sample plate.
Other methods of applying the specimen to the sample plate are also known. In the electrospray deposition method, the specimen is applied to the sample plate as a fine mist of microdroplets that evaporates very quickly forming the specimen crystals.
To analyze the biomolecules, the sample plate is inserted into the sampling compartment of a mass spectrometry instrument. A voltage is applied to the sample plate to permit the flow of electric current over the sample plate and prevent the possibility of an electrical charge buildup. To desorb the crystals, an ultra-violet (UV) laser scans the target area either by manual direction or in a predetermined automated fashion to irradiate the crystals. The laser beam radiation is absorbed by the matrix molecules, resulting in a vaporization of both the matrix molecules and the biomolecules. Once in the vapor phase, while still in close proximity to the target area, a charge transfer occurs as the matrix molecule loses a proton to the biomolecule. The ionized biomolecules are then drawn into the mass spectrometer where they are analyzed. Data processing yields a mass spectrum of a series of characteristic peaks corresponding to the biomolecules and matrix molecules. The signature of peaks is used to identify the biomolecules by reference to known peaks.
Prior art of interest includes U.S. Pat. No. 6,287,872 (herein incorporated by reference) relating to sample support plates for the mass spectrometric analysis of large molecules, such as biomolecules, methods for the manufacture of such sample support plates and methods for loading the sample support plates with samples of biomolecules from solutions together with matrix substance for the ionization of the biomolecules using matrix-assisted laser desorption (MALDI).
Also of interest is U.S. Pat. No. 5,958,345 (herein incorporated by reference) relating to a sample support for holding samples for use with an analysis instrument. The sample support is for use with analysis instruments, which rely on a beam of radiation or accelerated particles and a method for making the same. The holder includes a frame with one or more orifices covered by a support surface, typically in the form of a thin polymer film. The film is divided into hydrophobic and hydrophilic portions to isolate precise positions where samples can be placed to intersect a probe beam during analysis.
MALDI-MS performance suffers chiefly from analysis insensitivity. The sample plates that are used in MALDI-MS are typically metallic plates due to the need to apply a voltage across the plate. Known trays have a smooth hydrophilic surface where the applied specimen drop spreads over a relatively large area before drying and forming crystals. Consequently, to effectively irradiate the crystals the UV laser has to scan this enlarged area requiring extra time.
Another drawback of metallic plates is that they unfortunately often provide unsuitable results due to unintentional contamination from detergents. Since, metallic plates are also expensive, they are used repeatedly. Washing between each use may contaminate subsequent analysis.
It is known, that specimens are non-homogeneously distributed on and/or within the lattice that located at the specimen periphery. It is further known that some of these matrix crystals bear more biomolecules than others. Thus, as the laser covers a likely search area at the specimen periphery, it scans “sweet spots” having a comparatively higher specimen concentration in the matrices. When irradiated and detected, the sweet spots provide an inaccurate concentration reading of the biomolecule.
What is desired, therefore, is a sample plate for MALDI-MS analysis of a specimen wherein crystals are located in a sample site.
What is also desired is a durable and cost effective sample plate which enables archiving of samples.
What is also desired is a rough surface that is hydrophobic to enhance the formation of crystals in a sample site. What is further desired is a higher ratio of surface area to planar area of the hydrophobic mask.
Accordingly it is an object of the invention to provide a method of analyzing a specimen.
Another object of the invention is to provide a method of sample plate that overcomes known problems of analysis insensitivity.
A further object of the invention is to provide a sample plate wherein crystals are located at predetermined positions.
A still further object of the invention is to provide a durable and cost effective sample plate which enables archiving of samples.
These and other objects of the invention are achieved by a method that crystallizes analyte in a reduced area.
Therein, a method of scanning a sample plate surface mask in an area adjacent to a conductive area using mass spectrometry is disclosed. The method comprises the steps of providing a sample plate including a mask applied with a rough surface to the electrically conductive surface to produce a sample site comprising a central portion formed from the electrically conductive surface and a marginal portion of the mask, preparing an analyte comprising mixing a biomolecule with an organic solvent, an aqueous solution, and a matrix, applying the analyte to the sample site; forming at least one crystal of the analyte in an area on the mask adjacent to the conductive area, and scanning the area on the mask adjacent to the conductive area with a laser beam.
In some embodiment the step of scanning the area on the mask adjacent to the conductive area with a laser beam further comprises scanning in a pattern.
In some embodiments the method further comprises the step of determining a scanning pattern based on an algorithm having a confidence level.
In some embodiments the step of preparing a specimen further comprises providing a matrix selected from the group consisting of α-cyano-4-hydroxycinnamic acid and 3,5-dimethoxy-4-hydroxycinnamic acid.
In some embodiments the step of preparing a specimen further comprises providing an organic solvent.
In some embodiments the step of preparing a specimen further comprises providing an aqueous solution.
In some embodiments the step of preparing a specimen further comprises providing analyte wherein the analyte is at least one biomolecule.
In some embodiments the step of preparing a specimen further comprises providing analyte wherein the analyte is selected from the group consisting of oligonucleotides, DNA, RNA, peptide, polypeptide, oligopeptide, protein, glycoprotein, lipoprotein, carbohydrate, monosaccharide, disaccharide, polysaccharide, and mixtures thereof.
In some embodiments the method comprises applying a specimen to sample plate surface mask in an area adjacent to a conductive area comprising the steps of: providing a sample plate including a mask applied with a rough surface to an electrically conductive surface to produce a sample site comprising a central portion formed from the electrically conductive surface and a marginal portion of the mask; providing a liquid chromatography system for preparing a specimen comprising eluting a biomolecule with an organic solvent, an aqueous solution, and a matrix and applying the specimen; moving the sample plate cooperatively with the liquid chromatography system; and applying the specimen to the sample site.
In one embodiment, referred to for simplicity as a circle sample plate 10, and depicted in
Sample plate 10 is a sample plate for applying a sample containing both matrix and biomolecules, referred to for convenience as specimen 40 (not shown for clarity in
Sample plate 10 includes substrate 12 having electrically conductive surface 12 a and mask 14 which is selectively applied to surface 12 a to form a mask that has a rough surface 14 a where at least one target area 24 is located within sample site 20, as will be explained further herein.
Sample plate 10 is sized appropriately for usage for biological laboratory processing using automated and/or manual processing equipment. Thus, sample plate 10 may be appropriately sized as microtiter plate size comprising a rectangular plan size of 116.2 mm by 83 mm and/or any other convenient size. Sample plate 10 may be any suitable thickness for automated and/or manual processing. In accordance with one embodiment of the invention sample plate 10 is at minimum 0.5 mm thick with a maximum planar variance of 50 μm or less. For clarity, herein, sample plate 10 is described in relation to a rectangular plan and generally planar shape of the plate. However, sample plate 10 may have any plan shape and/or may have non-planar shapes as are and/or may become appropriate for usage.
In accordance with one embodiment of the invention, sample plate 10 has an indicator, such as a notched corner, that aids in orienting sample plate 10. Other indicators may instead or in addition be a central notch; one or more physical, chemical, optical, and/or electromagnetic markers; and/or any other type of indicator or indicating and/or orienting means.
In accordance with one embodiment of the invention, sample plate 10 has a reference indicator for inventorying or archiving sample plate 10 before and/or after usage. Such an indicator may be a bar tag, alpha-numeric reference, chemical and/or luminescent reference, and/or any indexing and/or archival reference that is readable by a machine and/or a human, attached to and/or integral with sample plate 10 on one or more of its surface.
In accordance with one embodiment of the invention, the reference indicator is sensitive to one or more wavelengths of the UV laser used in ionizing the crystals. Therein, the reference indicator is activated and/or marked by the UV laser leaving a permanent or semi-permanent reference readable by a machine and/or a human.
Substrate 12 is preferably substantially planar and is made of any solid material and/or combination of material. Substrate 12 has a first surface 12 a that is electrically conductive. Surface 12 a has an electrical resistance of 100 meg. ohms-per-square or less.
As illustrated in
Mask 14 is selectively applied to surface 12 a to form a mask that has a rough surface 14 a wherein target area 24 is centrally located within sample site 20. Preferably, mask 14 has a thickness in the range of 1 to 100 μm and is made of a material that is relatively more hydrophobic than surface 12 a and that maintains a suitable bond with substrate 12. For example, mask 14 may be made of polytetrafluoroethylene, commonly known as Teflon® and manufactured, sold, and/or licensed by DuPont Fluoroproducts of Wilmington, Del., or any other suitable material.
Rough surface 14 a is a non-homogenous surface that is characterized by a coarse and/or an uneven surface quality and that is lacking uniform surface intensity, regardless whether surface 14 a has a regular or repeating pattern or patterns of intensity, i.e. depth and/or graduations of the surface and/or material thickness.
In accordance with one embodiment of the invention, mask 14 may be adulterated, i.e. doped, with one or more marking agents that upon mass spectrometric analysis is/are detected as one or more markers as a predetermined analytical result or is detected by another means such as visual reference by an operator who sees the color effect of a marking agent. Such marking agents may be used for instrument calibration; quality assurance of sample preparation, handling, laboratory procedures, and/or sample tracking; quality assurance during production of sample plate 10; and/or handling. Examples of marking agents may be carbon black, titanium oxide, ferrous oxide, aluminum trioxides, polymeric materials, coloring materials, and/or others.
In accordance with one embodiment of the invention, mask 14 is applied to surface 12 a with a predetermined rough surface 14 a. For example, mask 14 is applied using a screening application process resulting in rough surface 14 a. Preferably, mask 14 is applied utilizing Teflon® with a screen mesh sizes ranging from 30×30 μm to 500×500 μm such resulting rough surface being described by the mesh size. Other screen sizes may be employed equally well. Upon screening, sample plate 10 is allowed to air dry, and once dry is heated to at least 50 Celsius to bond mask 14 with substrate 12. Referring to
In accordance with one embodiment of the invention, physical and/or chemical manipulation of the material of mask 14 is used to texture and create a rough surface 14 a. For example etching, gouging, scraping, oxidation, photo-oxidation, lithographic printing, off-set printing, reverse image accessing, and/or any other means may be used. In manufacturing the invention, rough surface may be applied to mask while mask is being applied to the substrate, or after it has been fixed to the surface.
Sample site 20 includes target area 24 and peripheral margin 22 of mask 14 that surrounds target area 24. Target area 24 is an area of electrically conductive surface 12 a and may have a number of equally preferred embodiments, including embodiments wherein target area 24 includes a mask spot or other structure. In accordance with one embodiment of the invention, target area 24 has a circular plan area as depicted in
As will be described further herein, target area 24 serves to substantially attract specimen 40 while it is in the liquid drop state. Specimen 40 is attracted to target area 24 because mask 14 is relatively more hydrophobic than target area 24.
In the circle sample plate 10 depicted in
As is easily understood, the volume of a drop of a liquid directly correlates to the diameter of any planar section of the drop. As is further understood, plan and radial dimensions of a drop of liquid may be predetermined by controlling the drop's volume and determining the relative hydrophilic and/or hydrophobic qualities of the surface to which it adheres. Thus, control of drop size may be achieved using pipetting or any other method to control the volume of specimen 40.
It is known that hydrophobic and/or hydrophilic qualities are relative to the contact angle between a drop and the surface to which it adheres. An angle of 0° indicates total hydrophilic wetting of the surface and an angle of 180° indicates total hydrophobicity of the surface. Teflon® typically has a contact angle of 140° to 160° for water.
In channel sample plate 10 depicted in
In accordance with one embodiment of the invention, sample site 20 includes target area 24 having a rectangular plan area.
In accordance with one embodiment of the invention, sample site 20 includes target area 24 having a curvilinear plan area comprising a spiral, although other curvilinear plan areas such as a series of concentric plan areas are also contemplated.
In accordance with one embodiment of the invention, mask 14 is additionally applied to a central region of target area 24 to form at least one mask spot 24 a.
Specimens 40, each consisting of a drop in liquid form, are applied to sample plate 10 within sample site 20 and contact mask 14. Therein, it is preferred that specimen 40 contact mask 14 at the sides over a distance of at least 0.1 mm.
For circle sample plate 10, specimen 40 contacts mask 14 in plan view at the perimeter of target area 24 by using a drop of specimen 40 where the drop's maximum diameter exceeds the diameter of target area 24. Since, it is known that a drop with a volume of 0.5 μl has diameter of approximately 1.0 mm on the hydrophobic surface of Teflon®, it is preferred that each specimen 40 is between 0.1 to 4.0 μl in volume.
For channel sample plate 10, specimen 40 contacts mask 14 in plan view at peripheral margin 22 while the perimeter of specimen 40 also contacts target area 24. In accordance with one embodiment of the invention, specimen 40 is applied within sample site 20 on channel sample plate 10 in a continuous manner, such as by spraying or streaking specimen 40. Therein, the width or length of the application of specimen 40 exceeds the width or length of target area 24, respectively, so that specimen 40 contacts mask 14.
In accordance with one embodiment of the invention, mask spot 24 a is appropriately sized to form a drop of specimen 40 so that the drop contacts the side of mask 14 to enhance the deposition of crystals.
Specimen 40 includes a biomolecule and a matrix mixed in a 1:1 ratio, by volume. Although other formulations including those with low solubility may also advantageously be used and the formulations presented herein are not intended to be limiting, the matrix may be made according to the following formulations:
In a first formulation (CHCA formulation), α-cyano-4-hydroxycinnamic acid (C10H7NO3) and an aqueous solution containing a solvent are mixed to produce a matrix. The solvent preferably is acetonitrile (C2H3N) and is mixed at a ratio of 30% to 50% acetonitrile and 70% to 50% water, respectively, with 0.1% trifluoroacetic acid (C2HF3O2), pH 2.3, by volume, to produce a solvent. CHCA may be present at a concentration of 0.2 mg to 20 mg per 1 ml of solvent, although a concentration of 1 to 5 mg of CHCA per 1 ml of solvent is preferred. The first formulation may utilize other matrices such as other cinnaminic acids or other matrices of low solubility instead of CHCA.
In a second formulation (SA formulation), 3,5-dimethoxy-4-hydroxycinnamic acid (C11H12O5), commonly known as sinapinic acid, and an aqueous solution containing a solvent are mixed to produce a matrix. The solvent preferably is acetonitrile (C2H3N) and is mixed at a ratio of 30% to 50% acetonitrile and 70% to 50% water with 0.1% trifluoroacetic acid (C2HF3O2), pH 2.3, by volume, to produce a solvent. Sinapinic acid may be present at a concentration of 0.2 mg to 20 mg per 1 ml of solvent, although a concentration of 1 to 5 mg of sinapinic acid per 1 ml of solvent is preferred.
The CHCA formulation is preferred for analysis of biomolecules such as peptides and other biomolecules having molecular weights of less than 10,000 Daltons. The SA formulation is preferred for biomolecules such as proteins and other biomolecules having molecular weights of 10,000 Daltons and more.
Crystal rings are believed to result from the increase in matrix concentration during the concomitant decrease in solvent volume as the solvent evaporates. Crystalline lattices begin to form and are attracted to rough surface 14 a known to induce crystalline formation. As the specimen drop dries, many matrix crystalline lattices precipitate from the solution at roughly the same time. Such precipitation occurs at regular intervals leading to deposition in ring. As the larger matrix crystals precipitate, smaller crystals form anew while the specimen drop continues drying. Eventually these smaller crystals 42 also are unsustainable in solution and precipitate from solution. In contrast, where a lower concentration of matrix is used, crystals 42 result in only one ring. Such crystals 42 are depicted in
To analyze the biomolecule, crystals 42 are irradiated using a UV laser (not shown for clarity) that scans crystals 42 directly using the energy of a laser beam. The UV laser generates a laser beam 48 typically at 337 nm wavelength, which may be any suitable ultra-violet laser beam such one having an effective beam diameter of 0.1 to 0.2 mm. As is easily understood, concentrating crystals 42 in margin 22 reduces the area required to be scanned by the laser in order to irradiate sufficient crystals 42 to obtain significant irradiation without compromising analysis sensitivity. Given the beam's relatively small effective diameter, reducing the requisite scanning area significantly enhances efficiency.
The reduced area is advantageously illustrated in comparison to the area that must be irradiated when a traditional formulation is used to produce specimen 40. To illustrate this example, 2,5-dihydroxybenzoic acid (C7H6O4) known as DHB is used and is compared to the formulations of the present invention. In DHB formulations, crystals 42 occur in target area 24. Thus, in order to irradiate crystals 42 of the DHB formulation, the entire target area 24 must be scanned. Thus, if target area 24 has a diameter of 1 mm, the area to be scanned is 0.25π mm2. In order to irradiate crystals 42 wherein the matrix is the CHCA or SA formulation and the sample site 20 has a diameter of 1.2 mm, the area to be scanned is the 0.11π mm2. This results in a required scanning area that is only 44% of the traditional scanning area.
Laser beam 48 sweeps scanning pattern 50 (not shown for clarity) wherein it irradiates crystals 42 at a first position, marked by the letter A in
One embodiment of scanning pattern 50 is illustrated in
For the cross pattern illustrated in
n=(3×r 1 2)/r 2 2 ×c Equation 1
where r1 is the radius of target area 24 and r2 is the effective radius of laser beam 48. Therein, if target area 24 is 1 mm in diameter, laser beam 48 has an effective diameter of 0.1 mm, and a confidence level of 75% is desired, 56.25 oscillation are required if boundaries 52 a and 52 b are at perimeters of margin 22.
Similarly, pattern 50 may be advantageously employed to more to reduce the time and travel of UV laser and more efficiently irradiate crystals 42 on a channel sample plate.
Therein, similarly, laser beam 48 utilizes pattern 50 that is confined by two predetermined boundaries; inner boundary 52 a that is approximate with the perimeter of target area 24 and an outer boundary 52 b that is within or coincident with sample site 20. Boundaries 52 a and 52 b may be predetermined according to experience by an operator, statistical sampling, by an algorithm, and/or any other suitable means. Illustrated in
In accordance with one embodiment of the invention, specimen 40 is applied on sample plate 10 using the electrospray deposition method. Critical to the electrospray deposition method is that specimen 40 is deposited in a smooth and constant application. Sample plate 10 moves on a platform while a liquid chromatography system elutes specimen 40 using a solvent and specimen 40 is applied by electrospray on sample plate 10 for mass spectrometry analysis.
Sample plate 10 is a channel sample plate or a circle sample plate and cooperatively progresses from one location to another with a liquid chromatography system. In accordance with one embodiment of the invention, sample plate is located on a moving platform that operates at a predetermined speed. Preferably, the platform is operator controllable and adjustable, and further includes one or more check mechanisms to ensure a precise predetermined speed that cooperates with the electrospray deposition.
A liquid chromatography system, such as micro-liquid chromatography system or nano-liquid chromatography system is provided to elute specimen 40 and apply it by electrospray on sample plate 10. Typically, the liquid chromatography system includes a reversed-phase column. The liquid chromatography system is eluted with a matrix of the CHCA formulation at a concentration of 1 mg of CHCA per 1 ml of solvent or SA formulation at a concentration of 1 mg of SA per 1 ml of solvent; although other matrices may also be used. Therein, the percentage of acetonitrile varies from 0% to 70% over the course of eluting specimen 40 from the column during the time period of elution, typically 15 to 60 minutes.
In accordance with one embodiment of the invention, specimen 40 is applied on channel sample plate 10 by direct application of specimen 40 in liquid form such as by streaking. Therein, sample plate 10 moves on a platform while a stationary liquid chromatography system applies specimen 40. Specimen 40 is applied to channel sample plate 10 at a continuous rate over a predetermined length of target area 24, preferably at a rate 1 μl per 1 mm of length of target area 24, while specimen 40 is applied to circle sample plate 10 at a rate consistent with the size of target area 24. Preferably, specimen 40 is applied within sample site 20 that is no more than 0.2 mm from the periphery of target area 24. Specimen 40 then quickly forms crystals 42 that deposit on rough surface 14 a from where they are irradiated using a UV laser.
The present novel invention is also contemplated in additional embodiments. In accordance with one embodiment of the invention, sample plate 10 is produced includes sample site 20 wherein mask 14 is selectively applied with rough surface 14 a to surface 12 a so that mask 14 is surrounded by surface 12 a. Specimen 40 may be applied to sample plate 10 using the dried droplet method by spotting, streaking, or spraying or by the electro-spray deposition method. Specimen 40 may also be applied by washing or submerging sample plate 10 with or in specimen 40. Crystals 42 will then form on mask 14 in peripheral margin 22 and may be efficiently irradiated using laser beam 48.
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|U.S. Classification||436/173, 435/287.8, 250/287, 436/174, 250/286, 250/281, 250/282|
|International Classification||G01N1/40, G01N24/00, G01N1/04, H01J49/00, G01N1/00, B01D59/44, B01L3/00, C12M3/00, C12M1/34|
|Cooperative Classification||B01L2300/0829, B01L3/5085, G01N2001/045, G01N1/40, H01J49/164, Y10T436/24, Y10T436/25, B01L3/5088, H01J49/0418, G01N2001/4027, B01L2300/165|
|European Classification||G01N1/40, H01J49/04E3, H01J49/16A3, B01L3/5088, B01L3/5085|
|Apr 30, 2003||AS||Assignment|
Owner name: PERKINELMER LAS, INC., MASSACHUSETTS
Free format text: ASSIGNMENT OF ASSIGNORS INTEREST;ASSIGNOR:DICESARE, JOSEPH L.;REEL/FRAME:014035/0522
Effective date: 20030210
|Nov 17, 2003||AS||Assignment|
Owner name: PERKINELMER INSTRUMENTS LLC, A DELAWARE LIMITED LI
Free format text: RE-RECORD TO CORRECT RECEIVING PARTY ON AN ASSIGNMENT DOCUMENT PREVIOUSLY RECORDED AT REEL/FRAME 014035/0522. RECEIVING PARTY WAS LISTED INCORRECTLY ON OUR COVER SHEET AND ON THE NOTICE OF RECORDATION AS PERKINELMER LAS, INC. THE CORRECT, RECEIVING PARTY IS PERKINELMER INSTRUMENTS LLC.;ASSIGNOR:DISCESARE, JOSEPH L.;REEL/FRAME:014697/0661
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